⚠️ SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026).
Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
Plotting:
- Base colours and legends of interpreted MIC and disk values on the interpretation itself instead of matching colours
- Fix SDD in autoplot() for disks, the colours of barplot() for SIR values, and barplot() for MICs ignoring language and expand
- Match a named colours_SIR by name; let keep_operators = TRUE/FALSE in scale_*_mic() behave as "all"/"none"
- Let a named values in scale_*_sir() replace the colours it names, warn in scale_x_sir(), and pass other arguments on
- Let the default of eucast_I follow the guideline option, also for EUCAST before 2019
- Support unquoted column names in facet_sir() without evaluating them
- Correct the documentation and examples
Translations:
- Add SDD, NS, WT and NWT, and correct S, I, R and NI in 18 languages
- Sources of the terms for 'I': NAK via German laboratories (de), SZU national reference laboratory (cs), lex.dk (da), Karolinska University Hospital (sv), COESANT (es), Nordlab (fi), CA-SFM (fr); no by analogy with da and sv
- Not verified against an official source: ar, bn, el, hi, id, ja, ko, pl, ro, ru, sw, tr, uk, ur, vi, zh
Tests:
- Let the grouped antibiogram test use English so it passes in other locales
WHONET names are now matched exactly (also outdated names, after removing qualifiers), then on GBIF identifier, and fuzzy results are only kept if consistent with that; otherwise the genus or UNKNOWN is used. A code refers to the record of the name it was named after (e.g. EAE is Enterobacter aerogenes) if that name refers to the same taxon. Every remap of an existing code to another taxon must be listed in data-raw/whonet_remaps_reviewed.csv; the 198 remaps of this rebuild were reviewed.
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
The pruning of blocking rows in the EUCAST reproduction script now compares UTI status too, and the script is fixed for the renamed column of the as.ab() coercion cache. In clinical_breakpoints, only the blocking rows were replaced (356 organism/agent/method combinations newly blocked, none unblocked); other changes of a full rebuild, caused by taxonomy updates in the WHONET-based rows, are not included.
- New sir_combine() to combine SIR results of multiple antimicrobials into one variable; antibiogram(), wisca() and the count/proportion functions now use the same engine (antibiogram() and wisca() output unchanged)
- With multiple antimicrobials, count_*() and proportion_*() now follow the documented combination therapy rules: resistance() is the proportion of failing combinations, count_all() excludes isolates with an unknown combination result, and WT/NWT/NS/NI are handled correctly
- where() is now decided at runtime instead of at installation, fixing antibiogram() and wisca() without tidyselect (e.g. CRAN binaries without dplyr)
- Imports from data.table and cli moved to .onLoad(); data.table functions are only used while it is loaded; the like() example no longer unloads data.table, which crashed R
- Static test that fails on code outside functions depending on suggested packages
- New check-without-dplyr workflow: installs AMR with all suggested packages, removes dplyr (and tidyselect), then runs all unit tests and examples against the installed package
- g.test() now returns the degrees of freedom as 'parameter', so they are printed
- Fix R CMD check NOTEs (hidden .claude folder, lost braces in inherited g.test and ggplot_pca docs)
Package:
- stop_() called cli::ansi_has_hyperlink_support() before checking that cli is available, so without cli every error became "there is no package called 'cli'"
- interpretive_rules() failed on R 3.0 for guidelines without AmpC rules (assignment to zero rows)
- Guard the ggplot2 example of wisca_plot()
CI:
- check-old: R 3.0 could not install tinytest over HTTPS, so no unit tests ran; install it with curl, and fail when tinytest is missing or any test fails
- tinytest shim: record expectations in the test file environment, support skips and errors per test_that() block, add missing testthat equivalents, source helper files
- Add R 4.0 (oldrel-6) to check-old, and oldrel-5 to check-recent
Adds add_custom_antimicrobial_synonyms() to add local names, such as trade names, to existing antimicrobials, also via the AMR_custom_ab option. Matching is language-independent; as.ab() now returns NA with a warning for input that is not valid UTF-8.
